[Bioc-devel] Best practice use pkgdown, docker with Bioconductor

[Murphy, Alan E]

Thank you all for your suggestions! Can anyone from the Bioconductor team comment on whether David's approach to use the .Rbuildignore file is valid for submission to Bioconductor? Obviously, this will would the least work so if possible, I would like to use this.

Kind regards,
Alan.
________________________________
From: David Jimenez-Morales <biodavidjm using gmail.com>
Sent: 06 April 2021 17:53
To: Andris Jankevics <A.Jankevics using bham.ac.uk>
Cc: Murphy, Alan E <a.murphy using imperial.ac.uk>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor


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Hi there,

What about including the "_pkgdown.yml" file in the ".Rbuildignore" file? Would this somehow help "avoiding any issues with these external configurations and Bioconductor"?

Thanks
David

On Tue, Apr 6, 2021 at 5:05 AM Andris Jankevics <A.Jankevics using bham.ac.uk<mailto:A.Jankevics using bham.ac.uk>> wrote:
Haven't used this, but I think you could use Github Action to merge master branch in the branch for pkgdown whenever changes on master are made.

https://github.com/marketplace/actions/merge-branch

BW,
Andris

-----Original Message-----
From: Bioc-devel <bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>> On Behalf Of Murphy, Alan E
Sent: 06 April 2021 16:24
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>
Subject: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor

Hi all,

I'm working on the development of (EWCE)[https://github.com/NathanSkene/EWCE] and have a question regarding a reviewer note. My package currently uses pkgdown to create a website through the master branch. I also create and push a new docker image from the main branch when the package successfully builds on travis.

My reviewer has asked to remove the related files _pkgdown.yml,Dockerfileanddocker_push from my master branch to avoid any issues with these external configurations and Bioconductor. My reviewer has suggested to put these in another branch. It's not clear to me how best to do this? Ideally, if they are in a separate branch, is there a way to run them once there is an update and successful build on the master branch? If this isn't possible, is there a way to avoid manually duplicating new changes in the master branch in this separate branch and instead, just push the changes from master to this separate branch and trigger pkgdown and docker build that way? Sorry, I realise this last part more so relates to github commands but I was thinking someone else has probably already foudn a way around this issue.

Kind regards,
Alan.

Alan Murphy
Bioinformatician
Neurogenomics lab
UK Dementia Research Institute
Imperial College London

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